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CONTRA for CNV detection. troubleshooting
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Entering edit mode
7.2 years ago
Kizuna ▴ 830

Hi Biostars Users,

I would like to know if you have encountered this issue while working with CONTRA tool http://sourceforge.net/apps/mediawiki/contra-cnv/index.php?title=CONTRA:_Copy_Number_Analysis_for_Targeted_Resequencing#Examples) for detecting CNVs in targeted NGS.

In fact, my analysis is "stopping" at the binning process with no error message, I have checked all the required arguments and they seem to be ok :

contra apple\$ python contra.py --target ngs1_probes.bed --test cic04668.bam --control  baseline_ngs1.bed --bed --fasta human_ref.fasta --outFolder ~/contrases


target              : ngs1_probes.bed

test                  : cic04668.bam

control                        : baseline_ngs1.bed

fasta                : human_ref.fasta

outfolder        : /Users/apple/contrases

numBin                       : [20]

minNBases     : 10

sam                 : False

pval                 : 0.05

sampleName  : No-SampleName

nomultimapped         : False

plot                 : False

bedInput                    : True

minExon                     : 2000

largeDeletion : False

Creating Output Folder :  Done.

Converting TEST Sample...

DEBUG 123 genomeCoverageBed -ibam cic04668.bam -bga -g /Users/apple/contrases/buf/sample.Genome

Converting CONTROL Sample...

Getting targeted regions DOC...

chr1

chr10

chr11

chr12

chr14

chr15

chr16

chr17

chr19

chr2

chr20

chr3

chr4

chr5

chr6

chr7

chr8

chr9

chrX

Targeted regions pre-processing: Done

Getting targeted regions DOC...

chr1

chr10

chr11

chr12

chr14

chr15

chr16

chr17

chr19

chr2

chr20

chr3

chr4

chr5

chr6

chr7

chr8

chr9

chrX

Targeted regions pre-processing: Done

Test file read depth =  97323185

Control file read depth         =  98289477

Pre-processing Completed.

Getting the Log Ratio

Binning….

Do you have any idea why ?

Kiz

next-gen sequencing genome software error cnv • 3.9k views
5
Entering edit mode
7.1 years ago
Kizuna ▴ 830

To be honest, I just dropped using CONTRA and I am currently using ExomeDepth from (R),

I have configured it and it is working really well (http://cran.r-project.org/web/packages/ExomeDepth/index.html ).. I advise you to use it, and if you need the scripts for CNVs detection, just tell me :)

I hope this helps,

Kizuna

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Entering edit mode

@Kizuna: I found out what the issue was in my case. Sharing it here just in case someone refers to this post. The issue with unlimited binning in my case was with --minExons.

--minExon

Minimum number of exons in one bin (if less than this number, bin that contains small number of exons will be merged to the adjacent bins) [Default : 2000]

There were only 800 exons in my targeted region. As this was less than defat value(2000) the tool kept looking for more 1600 exons to include in the bin. As they were not available it just kept binning for a really long time. I changed the option to --minExon=100 (running the 800 exons in 8 bins) and it worked fine.

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Entering edit mode

This was the problem in my case too, thank you for sharing this! very helpful!!

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Entering edit mode

Great~~worked for me. But changing thr --minExom provides the diffrent values in *.CNATable.10rd.10bases.20bins.txt file. Is it okay?

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Entering edit mode
7.1 years ago

Hello Kizauna,

I am new to CONTRA and I am facing the same problem. I have no idea what is wrong as there is no error message.   I am sure the thread is not stopped but it is running in my server for a couple of days. Were you able to resolve this.

0
Entering edit mode
6.6 years ago
Ettore Z ▴ 30

It could be a Python Memory Error issue. Try redirecting the standard error log in a file, i.e.

python contra.py --target ngs1_probes.bed --test cic04668.bam --control  baseline_ngs1.bed --bed --fasta human_ref.fasta --outFolder ~/contrases 2> error.log
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Entering edit mode
2.2 years ago
lffu_0032 ▴ 70

do not anyone think that the CONTRA's paper published in bioinfomatics is confusing? i read the paper but i think there are much logistic problem in the presentation or calculation.